It may help you to render content in your theme directly without the_content filter, although you would loose thigns like oembeds etc e.g.:
echo $post->post_content;
However this sounds like a symptom of a hack. If you have something complex like an embed then you should be using either oembed ( e.g. youtube, don’t be pasting the raw embed stuff ) or using a shortcode. Else there’s very, very few reasons to keep the html markup for things like p and br tags for ordinary content, and if you’re using div containers and other layout elements then you’re doing it wrong